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Release Announcement

We are pleased to announce the beta release of MGLTools 1.5.2 (including: PMV, ADT and VISION).

Installers for binary distributions are available for LINUX, Mac OS X and Windows at:http://mgltools.scripps.edu/downloads

The binary distributions contain:- a precompiled Python interpreter version 2.5; (Note: under windows the installer downloads and runs the Python 2.5 installer if it has not been installed previously)- PMV, ADT, VISION and all dependent Python packages.

UPDATE MECHANISM: - This distribution has an update mechanism for updating an installation with updates suitable for particular version. It also reports if a new release is available.

LICENSE AGREEMENTS:--------------------------------------The license agreements are provided on the download site athttp://mgltools.scripps.edu/downloads/license-agreementsand can also be found in the LICENSE file of the distribution.

NEW FEATURES AND BUG FIXES:--------------------------

ADT:

A major change is the introduction of 'modes' for ADT. The selected mode governs the commands available through the GUI menus which in turn governs the versions of input files generated. The default mode "AD4.0" produces files for AutoDock4. Available alternative modes are "AD3.05" which produces files for AutoDock3 and "AD4.1" which produces files for AutoDock41.

The current mode is displayed in a small window on the left of the ADT menubar. Double clicking on that small window opens a widget which allows the user to select a different mode. Changing the mode replaces the menuBar with one containing menus appropriate to the new mode.

Other changes include:

--AutoDockBondClassifier.py -added "detectAll" option to the CycleBondSelector this option enables detection of bonds formed by bonds between atoms in separate cycles

--ConfPlayer.py -added support for displaying ligand_efficiency in the information string for each conformation

--Conformation.py -added support for calculating ligand_efficiency which is binding_energy divided by the number of non-hydrogen atoms in the ligand, and attaching it to a conformation. -added property 'lenNonHAtoms' to the ligand molecule

--Docking.py -changed line 350 from version==4.0 to version>=4.0 to accommodate autodock41

--GridParameters.py -improved set_types_from_directory method: now npts is increased if any ligand in the directory has a dimension larger than npts for that dimension; previously this was done only for the single ligand updated write4 method: previously it forced the parameter_file value to be "AD4_parameters.dat" -updated write41 method: previously it forced the parameter_file value to be "AD4.1_bound.dat" -added first draft of method to produce AutoGrid41-style file: the key difference is inclusion of explicit specification of parameter_file 'AD4.1_bound.dat'. When AutoDock4.1 is released, AD4.1_bound.dat will be the default parameter library and included in the compilation process. With that version, it will no longer be necessary to specify an input parameter library file and have it located in the directory including the other input files.

--MoleculePreparation.py -added a voluminous verbose option to autoroot method of RotatableBondManager -changed RotatableBondManager so that it always uses the detectAll option of the AutoDockBondClassifier -fixed bug in writing flexible residue files: tyrosines were not formatted properly so that ATOM records directly followed ENDBRANCH records

--WebServices.py -modified to work with new adt modes

--XMLParser.py -added "about" keyword in parser dictionary for xml field -added tran0 in parser dictionary for xml field

--autoanalyze3Commands.py, autoanalyze4Commands.py, autoanalyze41Commands.py -added support for setting _showHistogram, _showDockingsAsSpheres, _showBindingSite, _chooseDockedConformations, _readDLG, _selectDLG and _makeSubsetClustering to AD3.05 version. These commands are called by other commands

--autoanalyzeCommands.py -added use of findGeomsByName so that displayInteractionsGeoms could be reused in autoanalyze3, autoanalyze4 and autoanalyze41 Commands

--autotorsCommands.py -added line 413 to make the rest of the menubar tan; -added updating analyze commands [showBindingSite,selectDLG, chooseDockedConformations, makeSubsetClustering] to updateCmds method -added using 'self.vf.GUI.VIEWER.findGeomsByName' to access markSph and rootSph to facilitate reuse of these geometries in the different versions of autotors

--__init__.py -added a method setADTmode which allows the user to select a mode for the ADT GUI

--Utilities24/prepare_flexreceptor4.py -added a comment which shows syntax for specifying more than one residue -added requirement that specified receptorfile be in .pdbqt format

--Utilities24/prepare_gpf4.py -moved lines setting the types from a directory (previously lines 108-109) BEFORE setting the flexible types to fix bug where flexible types were overwritten when a directory of ligands was used to set types

--Utilities24/write_largest_cluster_ligand.py -added casting a user-specified rms_tolerance to a float

--Utilities24/write_rigid_ligand.py -initial revision

PMV: - Pmv can now run without file writing permissions - _pmvrc: added repairCommands and superimposeCommandsNew to make them available by default - colorCommands.py: fixed bug #954 - cannot change colors with "choose color"!

Vision:

- now vision can run without file writing permissions - introduced "soft run" (run only what hasn't run yet) and "hard run" (re-run) - now "continuous run" (automatic run on new data) can be turned off - introduced automatic generation of OPAL Web Services nodes